PROSPER

In the past decades the study of human evolution has been expanded significantly through the addition of several biomolecular approaches. The palaeoproteomic analysis of skeletal material has recently emerged as one such novel biomolecular approach, as proteins preserve over longer time periods in mineralised tissues compared to DNA. Ancient protein sequences have been found to be phylogenetically informative, even for hominin fossils. As a result, palaeoproteomic analysis can be applied to skeletal material across the Pleistocene and can provide complementary molecular evidence on hominin evolutionary relationships on a global scale.

Like other methods to study ancient evolutionary relationships among hominin fossils, the palaeoproteomic approach comes with its own set of challenges. Palaeoanthropological and archaeological remains are rare and finite, and contain relatively small proteomes. They contain proteins that have been fragmented into short peptides and amino acids that have been heavily modified. To address these challenges, and realise the full potential of the palaeoproteomic approach, further proteomic methods need to be developed and optimised, and understanding of the biology of skeletal proteomes needs to be increased.

The PROSPER project aims to address these challenges found in palaeoproteomics and human evolutionary research.

Skeletal proteome variation

Sample selection is an important and highly relevant part of any destructive analysis. To expand our knowledge of skeletal proteomes, PROSPER aims to study the variation in the hominin skeletal proteome between and within different skeletal elements. This knowledge guides us in designing sampling strategies and sample selection from highly precious archaeological material, causing minimal alterations of the material.

Example publications:

Ásmundsdóttir et al., Composition variations in archaeological human bone proteomes (preprint).
Ásmundsdóttir et al., Early Holocene preservation differences between cortical and trabecular bone proteomes (Journal of Archaeological Science).

Skeletal sampling

Pleistocene skeletal specimens are precious, especially when it comes to hominin fossils. Sampling should therefore be as minimally invasive as possible, also for faunal remains. PROSPER aims to explore the potential of minimally invasive sampling approaches, accepting that the removal of any molecule from an archaeological skeletal specimen constitutes an invasive act.

Example publications:

Fagernäs et al., New methods on the block: taxonomic identification of archaeological bones in resin-embedded sediments through paleoproteomics (PNAS Nexus).
Hansen et al., A comparative study of commercially available, minimally invasive, sampling methods on Early Neolithic humeri analysed via palaeoproteomics (Journal of Archaeological Science).

Enhanced extraction approaches for Pleistocene skeletal proteomes

The PROSPER project aims to develop laboratory methods that will maximise proteome size and coverage of phylogenetically relevant proteins. With increased knowledge of hominin skeletal proteome and more robust laboratory methods, PROSPER aims to maximise the amount of information that can be extracted with minimal damage to irreplaceable fossils.

Example publications:

Fagernäs et al., Cleaning the dead: optimized decontamination enhances palaeoproteomic analyses of a Pleistocene hominin tooth from Khudji, Tajikistan (Journal of Archaeological Science).
Fagernäs et al., Digging deeper into ancient skeletal proteomes through consecutive digestion with multiple proteases (Journal of Proteomics)

Proteomic screening

Through proteomic screening approach, PROSPER aims to discover additional hominin specimens as well as provide additional palaeoecological and hominin subsistence strategy insights. We use both ZooMS (Zooarchaeology by Mass Spectrometry) as well as Species by Proteome Identification (SPIN) approaches. Aside from applying these methods, we also aim to improve their robustness as well as their sustainability.

Example publications:

Smith et al., The ecology, subsistence and diet of ~45,000-year-old Homo sapiens at Ilsenhöhle in Ranis, Germany (Nature Ecology & Evolution).
Mylopotamitaki et al., Comparing extraction efficiency for high-throughput palaeoproteomic bone species identification (Scientific Reports).
Le Meillour et al., Increasing sustainability in palaeoproteomics by optimizing digestion times for large-scale archaeological bone analyses (iScience).

Ancient hominin proteomes

The PROSPER project aims to study human evolution during the Middle and Late Pleistocene using phyloproteomic methods. The PROSPER project aims to analyze Middle and Late Pleistocene hominins that generally lack ancient DNA preservation, and sequence their proteomes using the improved sampling and extraction methods generated as part of the project. These proteomes will be highly informative to understand the emergence and distribution of archaic hominins as well as the association of particular hominin fossils to known (Neanderthals, Denisovans, modern humans) and unknown hominin lineages.

Example publications:

Tsutaya et al., A male Denisovan from Pleistocene Taiwan (Science).
Xia et al., Middle and Late Pleistocene Denisovan subsistence at Baishiya Karst Cave (Nature)

This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement #948365).

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